FeatureMapDF
- class pyopenms.dataframes.FeatureMapDF(*args, **kwargs)
Bases:
pyopenms.pyopenms_1.FeatureMap- __init__(*args, **kwargs)
Cython signature: void FeatureMap()
Cython signature: void FeatureMap(FeatureMap &)
Methods
__init__(*args, **kwargs)Cython signature: void FeatureMap()
Cython signature: void clear()
Cython signature: void clearMetaInfo() Removes all meta values
Cython signature: void clearRanges() Resets all range dimensions as empty
Cython signature: size_t clearUniqueId() Clear the unique id.
Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid.
Cython signature: libcpp_vector[DataProcessing] getDataProcessing()
Cython signature: String getIdentifier() Retrieve document identifier (e.g.
Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
Cython signature: String getLoadedFilePath() Returns the file_name which is the absolute path to the file loaded
Cython signature: int getLoadedFileType() Returns the file_type (e.g.
Cython signature: double getMaxIntensity() Returns the maximum intensity
Cython signature: double getMaxMZ() Returns the maximum m/z
Cython signature: double getMaxRT() Returns the maximum RT
Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
Cython signature: double getMinIntensity() Returns the minimum intensity
Cython signature: double getMinMZ() Returns the minimum m/z
Cython signature: double getMinRT() Returns the minimum RT
Cython signature: void getPrimaryMSRunPath(StringList & toFill) Returns the file path to the first MS run
Cython signature: libcpp_vector[ProteinIdentification] getProteinIdentifications()
Cython signature: libcpp_vector[PeptideIdentification] getUnassignedPeptideIdentifications()
Cython signature: size_t getUniqueId() Returns the unique id
Generates a list with peptide identifications assigned to a feature.
get_df([meta_values, ...])Generates a pandas DataFrame with information contained in the FeatureMap.
Cython signature: size_t hasInvalidUniqueId() Returns whether the unique id is invalid.
Cython signature: size_t hasValidUniqueId() Returns whether the unique id is valid.
Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
Cython signature: bool isValid(uint64_t unique_id) Returns true if the unique_id is valid, false otherwise
Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
Cython signature: void push_back(Feature spec)
Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
Cython signature: void setDataProcessing(libcpp_vector[DataProcessing]) Sets the description of the applied data processing
Cython signature: void setIdentifier(String id) Sets document identifier (e.g.
Cython signature: void setLoadedFilePath(String file_name) Sets the file_name according to absolute path of the file loaded, preferably done whilst loading
Cython signature: void setLoadedFileType(String file_name) Sets the file_type according to the type of the file loaded from, preferably done whilst loading
Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
Cython signature: void setPrimaryMSRunPath(StringList & s)
Cython signature: void setProteinIdentifications(libcpp_vector[ProteinIdentification]) Sets the protein identifications
Cython signature: void setUnassignedPeptideIdentifications(libcpp_vector[PeptideIdentification]) Sets the unassigned peptide identifications
Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id.
Cython signature: int size()
Cython signature: void sortByIntensity()
Cython signature: void sortByMZ() Sorts features by m/z position
Cython signature: void sortByOverallQuality() Sorts features by ascending overall quality.
Cython signature: void sortByPosition() Sorts features by position.
Cython signature: void sortByRT() Sorts features by RT position
Cython signature: void swap(FeatureMap &)
Cython signature: void swapFeaturesOnly(FeatureMap swapfrom) Swaps the feature content (plus its range information) of this map
Cython signature: void updateRanges()
- clear()
Cython signature: void clear() Clears all data and meta data
Cython signature: void clear(bool clear_meta_data) Clears all data and meta data. If ‘true’ is passed as an argument, all meta data is cleared in addition to the data
- clearMetaInfo()
Cython signature: void clearMetaInfo() Removes all meta values
- clearRanges()
Cython signature: void clearRanges() Resets all range dimensions as empty
- clearUniqueId()
Cython signature: size_t clearUniqueId() Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise
- ensureUniqueId()
Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise
- getDataProcessing()
Cython signature: libcpp_vector[DataProcessing] getDataProcessing()
- getIdentifier()
Cython signature: String getIdentifier() Retrieve document identifier (e.g. an LSID)
- getKeys()
Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
- getLoadedFilePath()
Cython signature: String getLoadedFilePath() Returns the file_name which is the absolute path to the file loaded
- getLoadedFileType()
Cython signature: int getLoadedFileType() Returns the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, …) of the file loaded
- getMaxIntensity()
Cython signature: double getMaxIntensity() Returns the maximum intensity
- getMaxMZ()
Cython signature: double getMaxMZ() Returns the maximum m/z
- getMaxRT()
Cython signature: double getMaxRT() Returns the maximum RT
- getMetaValue()
Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
- getMinIntensity()
Cython signature: double getMinIntensity() Returns the minimum intensity
- getMinMZ()
Cython signature: double getMinMZ() Returns the minimum m/z
- getMinRT()
Cython signature: double getMinRT() Returns the minimum RT
- getPrimaryMSRunPath()
Cython signature: void getPrimaryMSRunPath(StringList & toFill) Returns the file path to the first MS run
- getProteinIdentifications()
Cython signature: libcpp_vector[ProteinIdentification] getProteinIdentifications()
- getUnassignedPeptideIdentifications()
Cython signature: libcpp_vector[PeptideIdentification] getUnassignedPeptideIdentifications()
- getUniqueId()
Cython signature: size_t getUniqueId() Returns the unique id
- get_assigned_peptide_identifications()
Generates a list with peptide identifications assigned to a feature.
Adds ‘ID_native_id’ (feature spectrum id), ‘ID_filename’ (primary MS run path of corresponding ProteinIdentification) and ‘feature_id’ (unique ID of corresponding Feature) as meta values to the peptide hits. A DataFrame from the assigned peptides generated with peptide_identifications_to_df(assigned_peptides) can be merged with the FeatureMap DataFrame with: merged_df = pd.merge(feature_df, assigned_peptide_df, on=[‘feature_id’, ‘ID_native_id’, ‘ID_filename’])
Returns: [PeptideIdentification]: list of PeptideIdentification objects
- get_df(meta_values=None, export_peptide_identifications=True)
Generates a pandas DataFrame with information contained in the FeatureMap.
Optionally the feature meta values and information for the assigned PeptideHit can be exported.
Parameters: meta_values: meta values to include (None, [custom list of meta value names] or ‘all’)
export_peptide_identifications (bool): export sequence and score for best PeptideHit assigned to a feature. Additionally the ID_filename (file name of the corresponding ProteinIdentification) and the ID_native_id (spectrum ID of the corresponding Feature) are exported. They are also annotated as meta values when collecting all assigned PeptideIdentifications from a FeatureMap with FeatureMap.get_assigned_peptide_identifications(). A DataFrame from the assigned peptides generated with peptide_identifications_to_df(assigned_peptides) can be merged with the FeatureMap DataFrame with: merged_df = pd.merge(feature_df, assigned_peptide_df, on=[‘feature_id’, ‘ID_native_id’, ‘ID_filename’])
Returns: pandas.DataFrame: feature information stored in a DataFrame
- hasInvalidUniqueId()
Cython signature: size_t hasInvalidUniqueId() Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise
- hasValidUniqueId()
Cython signature: size_t hasValidUniqueId() Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise
- isMetaEmpty()
Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
- isValid()
Cython signature: bool isValid(uint64_t unique_id) Returns true if the unique_id is valid, false otherwise
- metaRegistry()
Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
- metaValueExists()
Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
- push_back()
Cython signature: void push_back(Feature spec)
Cython signature: void push_back(MRMFeature spec)
- removeMetaValue()
Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
- setDataProcessing()
Cython signature: void setDataProcessing(libcpp_vector[DataProcessing]) Sets the description of the applied data processing
- setIdentifier()
Cython signature: void setIdentifier(String id) Sets document identifier (e.g. an LSID)
- setLoadedFilePath()
Cython signature: void setLoadedFilePath(String file_name) Sets the file_name according to absolute path of the file loaded, preferably done whilst loading
- setLoadedFileType()
Cython signature: void setLoadedFileType(String file_name) Sets the file_type according to the type of the file loaded from, preferably done whilst loading
- setMetaValue()
Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
- setPrimaryMSRunPath()
Cython signature: void setPrimaryMSRunPath(StringList & s) Sets the file path to the primary MS run (usually the mzML file obtained after data conversion from raw files)
Cython signature: void setPrimaryMSRunPath(StringList & s, MSExperiment & e) Sets the file path to the primary MS run using the mzML annotated in the MSExperiment argument e
- setProteinIdentifications()
Cython signature: void setProteinIdentifications(libcpp_vector[ProteinIdentification]) Sets the protein identifications
- setUnassignedPeptideIdentifications()
Cython signature: void setUnassignedPeptideIdentifications(libcpp_vector[PeptideIdentification]) Sets the unassigned peptide identifications
- setUniqueId()
Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id. Always returns 1
- setUniqueIds()
- size()
Cython signature: int size()
- sortByIntensity()
Cython signature: void sortByIntensity() Sorts the peaks according to ascending intensity
Cython signature: void sortByIntensity(bool reverse) Sorts the peaks according to ascending intensity. Order is reversed if argument is true ( reverse = true )
- sortByMZ()
Cython signature: void sortByMZ() Sorts features by m/z position
- sortByOverallQuality()
Cython signature: void sortByOverallQuality() Sorts features by ascending overall quality. Order is reversed if argument is true ( reverse = true )
- sortByPosition()
Cython signature: void sortByPosition() Sorts features by position. Lexicographical comparison (first RT then m/z) is done
- sortByRT()
Cython signature: void sortByRT() Sorts features by RT position
- swap()
Cython signature: void swap(FeatureMap &)
- swapFeaturesOnly()
Cython signature: void swapFeaturesOnly(FeatureMap swapfrom) Swaps the feature content (plus its range information) of this map
- updateRanges()
Cython signature: void updateRanges()